ImportError

[lblaabjerg]

Hi,

When I try to run from moleculekit.occupancy_utils import calculate_occupancy I get an import error:

ImportError: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages/moleculekit/occupancy_utils.cpython-37m-x86_64-linux-gnu.so)

My glibc version is 2.17, HTMD version is 2.0.6 with Python 3.7 installed in a fresh Miniconda environment. This is a follow-up question to: https://github.com/Acellera/htmd/issues/1043.

Thank you in advance.

[stefdoerr]

Your operating system is too old. Older moleculekit versions were compiled unfortunately under a recent Ubuntu version and thus are not backwards compatible. In new moleculekit versions I compile them under a very old OS so that they are backwards compatible. This practically leaves us only with the option of you compiling moleculekit manually. It's not too tricky though. Do the following while having the HTMD conda environment active

conda list moleculekit # get the version from here
git clone https://github.com/Acellera/moleculekit
cd moleculekit
git checkout VERSION_FROM_ABOVE_COMMAND
pip install .

This should re-compile all the cython modules with your system's glibc version.

[lblaabjerg]

Thanks Stefan. I tried following your instructions and now get this error:

(thermonet) [lasbla@s96n41 moleculekit]$ git checkout 1.3.4 Checking out files: 100% (158/158), done. Note: checking out '1.3.4'.

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:

git checkout -b new_branch_name

HEAD is now at c7a8e52... remove offending line (thermonet) [lasbla@s96n41 moleculekit]$ pip install . Processing /home/lasbla/moleculekit Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: tqdm in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from moleculekit==1.3.4) (4.64.1) Requirement already satisfied: mmtf-python in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from moleculekit==1.3.4) (1.1.3) Requirement already satisfied: scipy in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from moleculekit==1.3.4) (1.7.3) Requirement already satisfied: networkx in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from moleculekit==1.3.4) (2.7) Requirement already satisfied: numpy>=1.17 in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from moleculekit==1.3.4) (1.21.6) Requirement already satisfied: pandas>=1.1.2 in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from moleculekit==1.3.4) (1.3.5) Requirement already satisfied: python-dateutil>=2.7.3 in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from pandas>=1.1.2->moleculekit==1.3.4) (2.8.2) Requirement already satisfied: pytz>=2017.3 in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from pandas>=1.1.2->moleculekit==1.3.4) (2022.6) Requirement already satisfied: msgpack>=1.0.0 in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from mmtf-python->moleculekit==1.3.4) (1.0.4) Requirement already satisfied: six>=1.5 in /home/lasbla/miniconda3/envs/thermonet/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas>=1.1.2->moleculekit==1.3.4) (1.16.0) Building wheels for collected packages: moleculekit Building wheel for moleculekit (pyproject.toml) ... error error: subprocess-exited-with-error

× Building wheel for moleculekit (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [573 lines of output] running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-37 creating build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/config.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/dihedral.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/pymolgraphics.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/rcsb.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/rdkitintegration.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/version.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/viewer.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/vmdgraphics.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/vmdviewer.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/align.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/bondguesser.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/home.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/molecule.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/periodictable.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/readers.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/util.py -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/writers.py -> build/lib.linux-x86_64-cpython-37/moleculekit creating build/lib.linux-x86_64-cpython-37/moleculekit/atomselect copying moleculekit/atomselect/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/atomselect copying moleculekit/atomselect/analyze.py -> build/lib.linux-x86_64-cpython-37/moleculekit/atomselect copying moleculekit/atomselect/atomselect.py -> build/lib.linux-x86_64-cpython-37/moleculekit/atomselect copying moleculekit/atomselect/languageparser.py -> build/lib.linux-x86_64-cpython-37/moleculekit/atomselect creating build/lib.linux-x86_64-cpython-37/moleculekit/interactions copying moleculekit/interactions/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/interactions copying moleculekit/interactions/interactions.py -> build/lib.linux-x86_64-cpython-37/moleculekit/interactions creating build/lib.linux-x86_64-cpython-37/moleculekit/pdbx copying moleculekit/pdbx/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx creating build/lib.linux-x86_64-cpython-37/moleculekit/ply copying moleculekit/ply/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/ply copying moleculekit/ply/lex.py -> build/lib.linux-x86_64-cpython-37/moleculekit/ply copying moleculekit/ply/yacc.py -> build/lib.linux-x86_64-cpython-37/moleculekit/ply creating build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricdihedral.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricfluctuation.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricgyration.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricplumed2.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricrmsd.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricsecondarystructure.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricshell.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricsphericalcoordinate.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/projection.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metriccoordinate.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricdistance.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metricsasa.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/metrictmscore.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections copying moleculekit/projections/util.py -> build/lib.linux-x86_64-cpython-37/moleculekit/projections creating build/lib.linux-x86_64-cpython-37/moleculekit/smallmol copying moleculekit/smallmol/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol copying moleculekit/smallmol/test_smallmol.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol copying moleculekit/smallmol/test_smallmollib.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol copying moleculekit/smallmol/util.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol copying moleculekit/smallmol/smallmol.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol copying moleculekit/smallmol/smallmollib.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol creating build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/atomtyper.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/autosegment.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/crystalpacking.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/docking.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/graphalignment.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/hhblitsprofile.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/moleculechecks.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/preparation_customres.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/voxeldescriptors.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/detect.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/preparation.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools copying moleculekit/tools/sequencestructuralalignment.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools creating build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/reader copying moleculekit/pdbx/reader/PdbxContainers.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/reader copying moleculekit/pdbx/reader/PdbxParser.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/reader copying moleculekit/pdbx/reader/PdbxReader.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/reader copying moleculekit/pdbx/reader/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/reader creating build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/writer copying moleculekit/pdbx/writer/PdbxWriter.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/writer copying moleculekit/pdbx/writer/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/pdbx/writer creating build/lib.linux-x86_64-cpython-37/moleculekit/smallmol/tools copying moleculekit/smallmol/tools/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol/tools copying moleculekit/smallmol/tools/clustering.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol/tools copying moleculekit/smallmol/tools/restrainedembed.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol/tools copying moleculekit/smallmol/tools/test_tools.py -> build/lib.linux-x86_64-cpython-37/moleculekit/smallmol/tools creating build/lib.linux-x86_64-cpython-37/moleculekit/tools/obabel_tools copying moleculekit/tools/obabel_tools/init.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools/obabel_tools copying moleculekit/tools/obabel_tools/obabel_cli.py -> build/lib.linux-x86_64-cpython-37/moleculekit/tools/obabel_tools copying moleculekit/vmd_wrapper -> build/lib.linux-x86_64-cpython-37/moleculekit copying moleculekit/logging.ini -> build/lib.linux-x86_64-cpython-37/moleculekit creating build/lib.linux-x86_64-cpython-37/moleculekit/share creating build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr creating build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/004.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/004.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/03Y.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/03Y.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/0A1.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/0A1.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/0AF.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/0AF.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/0BN.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/0BN.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/1MH.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/1MH.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2AS.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2AS.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2GX.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2GX.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2ML.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2ML.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2MR.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/2MR.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/4IN.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/4IN.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/4PH.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/4PH.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/5JP.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/5JP.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/AA4.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/AA4.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ABA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ABA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/AHP.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/AHP.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ALC.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ALC.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ALN.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ALN.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ALY.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ALY.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/APD.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/APD.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/BB8.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/BB8.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/BCS.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/BCS.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/BTK.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/BTK.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CCS.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CCS.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CGU.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CGU.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSO.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSO.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSP.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSP.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSS.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/CSS.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/D4P.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/D4P.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DA2.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DA2.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DAB.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DAB.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DAH.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DAH.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DPP.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/DPP.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ESC.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ESC.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/FGL.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/FGL.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/GHG.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/GHG.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/GME.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/GME.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/GNC.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/GNC.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HHK.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HHK.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HLU.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HLU.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HLX.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HLX.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HOX.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HOX.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HPE.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HPE.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HQA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HQA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HTR.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HTR.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HYP.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/HYP.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/I2M.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/I2M.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/IGL.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/IGL.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/IIL.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/IIL.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/IML.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/IML.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/KYN.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/KYN.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/LME.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/LME.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/M3L.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/M3L.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ME0.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ME0.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MEA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MEA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MEN.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MEN.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MLE.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MLE.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MLY.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MLY.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MME.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MME.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MMO.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MMO.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MVA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/MVA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NAL.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NAL.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NCY.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NCY.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NLE.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NLE.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NVA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NVA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NZC.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/NZC.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/OCY.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/OCY.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/OMX.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/OMX.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ONL.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ONL.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ORM.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/ORM.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/P1L.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/P1L.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/PCA.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/PCA.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/PRK.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/PRK.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/PTR.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/PTR.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/SEP.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/SEP.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TPO.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TPO.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TRO.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TRO.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TY2.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TY2.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/YCM.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/YCM.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/YNM.dat -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues copying moleculekit/share/pdb2pqr/residues/YNM.xml -> build/lib.linux-x86_64-cpython-37/moleculekit/share/pdb2pqr/residues creating build/lib.linux-x86_64-cpython-37/moleculekit/share/atomselect copying moleculekit/share/atomselect/atomselect.json -> build/lib.linux-x86_64-cpython-37/moleculekit/share/atomselect copying moleculekit/share/ALA.cif -> build/lib.linux-x86_64-cpython-37/moleculekit/share copying moleculekit/share/backbone.cif -> build/lib.linux-x86_64-cpython-37/moleculekit/share running build_ext building 'moleculekit.interactions.hbonds' extension creating build/temp.linux-x86_64-cpython-37 creating build/temp.linux-x86_64-cpython-37/moleculekit creating build/temp.linux-x86_64-cpython-37/moleculekit/interactions creating build/temp.linux-x86_64-cpython-37/moleculekit/interactions/hbonds gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/interactions/hbonds/hbonds.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/interactions/hbonds/hbonds.o -O3 cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default] In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0, from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from moleculekit/interactions/hbonds/hbonds.cpp:786: /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it with " \

    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/interactions/hbonds/hbonds.o -o build/lib.linux-x86_64-cpython-37/moleculekit/interactions/hbonds.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.interactions.pipi' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/interactions/pipi
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/interactions/pipi/pipi.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/interactions/pipi/pipi.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/interactions/pipi/pipi.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/interactions/pipi/pipi.o -o build/lib.linux-x86_64-cpython-37/moleculekit/interactions/pipi.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.interactions.cationpi' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/interactions/cationpi
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/interactions/cationpi/cationpi.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/interactions/cationpi/cationpi.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/interactions/cationpi/cationpi.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/interactions/cationpi/cationpi.o -o build/lib.linux-x86_64-cpython-37/moleculekit/interactions/cationpi.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.interactions.sigmahole' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/interactions/sigmahole
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/interactions/sigmahole/sigmahole.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/interactions/sigmahole/sigmahole.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/interactions/sigmahole/sigmahole.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/interactions/sigmahole/sigmahole.o -o build/lib.linux-x86_64-cpython-37/moleculekit/interactions/sigmahole.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.wrapping' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/wrapping
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/wrapping/wrapping.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/wrapping/wrapping.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/wrapping/wrapping.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/wrapping/wrapping.o -o build/lib.linux-x86_64-cpython-37/moleculekit/wrapping.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.bondguesser_utils' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/bondguesser_utils
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/bondguesser_utils/bondguesser_utils.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/bondguesser_utils/bondguesser_utils.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/bondguesser_utils/bondguesser_utils.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp: In function 'PyObject* __pyx_pf_11moleculekit_17bondguesser_utils_make_grid_neighborlist_nonperiodic(PyObject*, __Pyx_memviewslice, __pyx_t_11moleculekit_17bondguesser_utils_UINT32_t, __pyx_t_11moleculekit_17bondguesser_utils_UINT32_t, __pyx_t_11moleculekit_17bondguesser_utils_UINT32_t)':
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:2954:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
                                     ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:2966:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                                       ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:2978:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
                                         ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3017:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_12 = ((__pyx_v_xi < (__pyx_v_xboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3056:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_12 = ((__pyx_v_yi < (__pyx_v_yboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3095:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_12 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3134:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_xi < (__pyx_v_xboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3140:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_yi < (__pyx_v_yboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3181:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_xi < (__pyx_v_xboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3187:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3228:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_yi < (__pyx_v_yboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3234:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3275:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_xi < (__pyx_v_xboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3328:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3375:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3416:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_xi < (__pyx_v_xboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3422:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_yi < (__pyx_v_yboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3428:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3475:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_yi < (__pyx_v_yboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3481:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3522:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_xi < (__pyx_v_xboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3534:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:3587:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_13 = ((__pyx_v_zi < (__pyx_v_zboxes - 1)) != 0);
                                                          ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp: In function 'PyObject* __pyx_pf_11moleculekit_17bondguesser_utils_2grid_bonds(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float, int, __Pyx_memviewslice, __Pyx_memviewslice)':
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:4136:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         __pyx_t_6 = ((__pyx_v_boxneigh == __pyx_v_n_boxes) != 0);
                                           ^
  moleculekit/bondguesser_utils/bondguesser_utils.cpp:4173:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         __pyx_t_6 = ((__pyx_v_boxneigh == __pyx_v_boxidx) != 0);
                                           ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/bondguesser_utils/bondguesser_utils.o -o build/lib.linux-x86_64-cpython-37/moleculekit/bondguesser_utils.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.atomselect_utils' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/atomselect_utils
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/atomselect_utils/atomselect_utils.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/atomselect_utils/atomselect_utils.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/atomselect_utils/atomselect_utils.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  moleculekit/atomselect_utils/atomselect_utils.cpp: In function 'bool __pyx_f_11moleculekit_16atomselect_utils__find_connected_subfragment(int, int, const char*, const char*, const char*, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, std::vector<std::basic_string<char> >&, __Pyx_memviewslice, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&)':
  moleculekit/atomselect_utils/atomselect_utils.cpp:5406:165: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         __pyx_t_3 = (((*((__pyx_t_11moleculekit_16atomselect_utils_UINT32_t *) ( /* dim=0 */ (__pyx_v_uq_resid.data + __pyx_t_2 * __pyx_v_uq_resid.strides[0]) ))) != __pyx_v_resnum) != 0);
                                                                                                                                                                       ^
  moleculekit/atomselect_utils/atomselect_utils.cpp: In function 'bool __pyx_f_11moleculekit_16atomselect_utils__find_subfragments(int, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, std::vector<std::basic_string<char> >&, __Pyx_memviewslice, std::vector<std::vector<int> >&)':
  moleculekit/atomselect_utils/atomselect_utils.cpp:5660:167: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_6 = (((*((__pyx_t_11moleculekit_16atomselect_utils_UINT32_t *) ( /* dim=0 */ (__pyx_v_uq_resid.data + __pyx_t_5 * __pyx_v_uq_resid.strides[0]) ))) != __pyx_v_i) != 0);
                                                                                                                                                                         ^
  moleculekit/atomselect_utils/atomselect_utils.cpp: In function 'bool __pyx_f_11moleculekit_16atomselect_utils__find_subfragments_topologically(int, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, std::vector<std::basic_string<char> >&, __Pyx_memviewslice, std::vector<std::vector<int> >&)':
  moleculekit/atomselect_utils/atomselect_utils.cpp:5926:167: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           __pyx_t_6 = (((*((__pyx_t_11moleculekit_16atomselect_utils_UINT32_t *) ( /* dim=0 */ (__pyx_v_uq_resid.data + __pyx_t_5 * __pyx_v_uq_resid.strides[0]) ))) != __pyx_v_i) != 0);
                                                                                                                                                                         ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/atomselect_utils/atomselect_utils.o -o build/lib.linux-x86_64-cpython-37/moleculekit/atomselect_utils.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.distance_utils' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/distance_utils
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/distance_utils/distance_utils.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/distance_utils/distance_utils.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/distance_utils/distance_utils.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/distance_utils/distance_utils.o -o build/lib.linux-x86_64-cpython-37/moleculekit/distance_utils.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.occupancy_utils' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/occupancy_utils
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/occupancy_utils/occupancy_utils.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/occupancy_utils/occupancy_utils.o -O3
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/occupancy_utils/occupancy_utils.cpp:786:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  g++ -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/occupancy_utils/occupancy_utils.o -o build/lib.linux-x86_64-cpython-37/moleculekit/occupancy_utils.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.xtc' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils
  creating build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Imoleculekit/xtc_utils/include/ -Imoleculekit/xtc_utils/ -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/xtc_utils/src/xdrfile.c -o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
  moleculekit/xtc_utils/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
  moleculekit/xtc_utils/src/xdrfile.c:763:6: warning: unused variable 'errval' [-Wunused-variable]
    int errval=1;
        ^
  moleculekit/xtc_utils/src/xdrfile.c:759:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
    int smallnum, smaller, larger, i, is_smaller, run;
                           ^
  moleculekit/xtc_utils/src/xdrfile.c:756:17: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
    int smallidx,  minidx, maxidx;
                   ^
  moleculekit/xtc_utils/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
  moleculekit/xtc_utils/src/xdrfile.c:1001:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
    int errval;
        ^
  moleculekit/xtc_utils/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
  moleculekit/xtc_utils/src/xdrfile.c:1297:6: warning: unused variable 'errval' [-Wunused-variable]
    int errval=1;
        ^
  moleculekit/xtc_utils/src/xdrfile.c:1292:25: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
    int smallnum, smaller, larger, i, is_smaller, run;
                           ^
  moleculekit/xtc_utils/src/xdrfile.c:1289:25: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
    int smallidx,  maxidx, minidx;
                           ^
  moleculekit/xtc_utils/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
  moleculekit/xtc_utils/src/xdrfile.c:1504:6: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
    int errval=1;
        ^
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Imoleculekit/xtc_utils/include/ -Imoleculekit/xtc_utils/ -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/xtc_utils/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Imoleculekit/xtc_utils/include/ -Imoleculekit/xtc_utils/ -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/xtc_utils/src/xtc.c -o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
  moleculekit/xtc_utils/src/xtc.c: In function 'xtc_read_new':
  moleculekit/xtc_utils/src/xtc.c:201:6: warning: unused variable 'nf3' [-Wunused-variable]
    int nf3 = nframes * 3; // Precalculate 3 * nframes for the coordinate lookup macro
        ^
  moleculekit/xtc_utils/src/xtc.c: In function 'xtc_write':
  moleculekit/xtc_utils/src/xtc.c:416:6: warning: unused variable 'nf3' [-Wunused-variable]
    int nf3 = nframes * 3;
        ^
  moleculekit/xtc_utils/src/xtc.c: In function 'xtc_read_frame':
  moleculekit/xtc_utils/src/xtc.c:500:3: warning: 'return' with a value, in function returning void [enabled by default]
     return NULL;
     ^
  moleculekit/xtc_utils/src/xtc.c:581:4: warning: 'return' with a value, in function returning void [enabled by default]
      return NULL;
      ^
  moleculekit/xtc_utils/src/xtc.c:586:4: warning: 'return' with a value, in function returning void [enabled by default]
      return NULL;
      ^
  moleculekit/xtc_utils/src/xtc.c:597:4: warning: 'return' with a value, in function returning void [enabled by default]
      return NULL;
      ^
  moleculekit/xtc_utils/src/xtc.c:605:4: warning: 'return' with a value, in function returning void [enabled by default]
      return NULL;
      ^
  moleculekit/xtc_utils/src/xtc.c:641:2: warning: 'return' with a value, in function returning void [enabled by default]
    return frames;
    ^
  moleculekit/xtc_utils/src/xtc.c:495:6: warning: unused variable 'writing_index' [-Wunused-variable]
    int writing_index = 0;
        ^
  moleculekit/xtc_utils/src/xtc.c:494:6: warning: unused variable 'reading_index' [-Wunused-variable]
    int reading_index = 0;
        ^
  moleculekit/xtc_utils/src/xtc.c:539:10: warning: 'garbage_natoms' may be used uninitialized in this function [-Wmaybe-uninitialized]
     frames = xtc_read(filename, garbage_natoms, &traj_nframes, &dt, &dstep);
            ^
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Imoleculekit/xtc_utils/include/ -Imoleculekit/xtc_utils/ -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/xtc_utils/xtc.c -o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
  In file included from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969:0,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from moleculekit/xtc_utils/xtc.c:778:
  /tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  gcc -pthread -shared -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -L/home/lasbla/miniconda3/envs/thermonet/lib -Wl,-rpath=/home/lasbla/miniconda3/envs/thermonet/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src/xdrfile.o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/src/xtc.o build/temp.linux-x86_64-cpython-37/moleculekit/xtc_utils/xtc.o -o build/lib.linux-x86_64-cpython-37/moleculekit/xtc.cpython-37m-x86_64-linux-gnu.so
  building 'moleculekit.tmalign' extension
  creating build/temp.linux-x86_64-cpython-37/moleculekit/tmalign
  creating build/temp.linux-x86_64-cpython-37/moleculekit/tmalign/src
  gcc -pthread -B /home/lasbla/miniconda3/envs/thermonet/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Imoleculekit/tmalign/include/ -Imoleculekit/tmalign/ -I/tmp/pip-build-env-o34rs6hk/overlay/lib/python3.7/site-packages/numpy/core/include -I/home/lasbla/miniconda3/envs/thermonet/include/python3.7m -c moleculekit/tmalign/src/TMAlign.cpp -o build/temp.linux-x86_64-cpython-37/moleculekit/tmalign/src/TMAlign.o -w
  cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
  moleculekit/tmalign/src/TMAlign.cpp:450:42: error: '>>' should be '> >' within a nested template argument list
                        vector<vector<string>> &PDB_lines, vector<string> &chainID_list,
                                            ^
  moleculekit/tmalign/src/TMAlign.cpp:847:44: error: '>>' should be '> >' within a nested template argument list
                          vector<vector<string>> &FASTA_lines, vector<string> &chainID_list,
                                              ^
  moleculekit/tmalign/src/TMAlign.cpp: In function 'int main(int, char**)':
  moleculekit/tmalign/src/TMAlign.cpp:5317:25: error: '>>' should be '> >' within a nested template argument list
       vector<vector<string>> PDB_lines1; // text of chain1
                           ^
  moleculekit/tmalign/src/TMAlign.cpp:5318:25: error: '>>' should be '> >' within a nested template argument list
       vector<vector<string>> PDB_lines2; // text of chain2
                           ^
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for moleculekit Failed to build moleculekit ERROR: Could not build wheels for moleculekit, which is required to install pyproject.toml-based projects

[stefdoerr]

That is fixed on master https://github.com/Acellera/moleculekit/blob/main/moleculekit/tmalign/src/TMAlign.cpp#L450 Overwrite your TMAlign.cpp file with the one linked here and try again.